huangziwei

import zipfile

zout = zipfile.ZipFile('nmf.zip', "w", zipfile.ZIP_DEFLATED) # <--- this is the change you need to make
zout.write('nmf.h5')
zout.close()

huangziwei

huangziwei

soffice --headless --convert-to xlsx:"Calc MS Excel 2007 XML" *.csv --outdir <output folder>

huangziwei

#!/bin/bash

apt-get update
apt-get upgrade -y
apt-get install -y autoconf libtool libxext-dev libncurses5-dev bison flex apt-utils wget
cd $HOME
git clone https://github.com/nrnhines/nrn
cd nrn
./build.sh
./configure --prefix=`pwd` --with-nrnpython=/usr/bin/python3 --without-iv

huangziwei

#!/bin/bash

sudo apt-get update
sudo apt-get install -y libxext-dev libncurses5-dev autoconf libtool bison flex

cd ~
git clone https://github.com/nrnhines/nrn
cd nrn
./build.sh
./configure --prefix=`pwd` --with-nrnpython=python3 --without-iv

huangziwei

def unique_row(a):
    
    b = np.ascontiguousarray(a).view(np.dtype((np.void, a.dtype.itemsize * a.shape[1])))
    _, idx = np.unique(b, return_index=True)
    
    unique_a = a[idx]
    
    return unique_a

huangziwei

def lfactorial(n):
  
    from scipy.special import gammaln
  
    return gammaln(n+1)


def lchoose(n, k):
  
    from scipy.special import gammaln

huangziwei

#!/bin/bash

git clone https://github.com/pyenv/pyenv .pyenv
echo 'export PYENV_ROOT="/.pyenv"' >> ~/.bashrc
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(pyenv init -)"' >> ~/.bashrc
exec $SHELL
pyenv install miniconda3-latest 
pyenv shell miniconda3-latest
conda install numpy scipy jupyter matplotlib scikit-learn

huangziwei

def load_h5_data(file_name):
    with h5py.File(file_name,'r') as f:
        return {key:f[key][:] for key in list(f.keys())}
    
def detect_soma_centroid(M):
    
    """
    detect the coordinate of soma on stack image.
    
    Return

huangziwei

def rotate_roi(d):
    
    ang_deg = d['wParamsNum'][31] # ratoate angle (degree)
    ang_rad = ang_deg * np.pi / 180 # ratoate angle (radian)
    
    d_rois = d['ROIs']
    d_rois_rot = scipy.ndimage.interpolation.rotate(d_rois, ang_deg)
    
    (shift_x, shift_y) = 0.5 * (np.array(d_rois_rot.shape) - np.array(d_rois.shape))
    (cx, cy) = 0.5 * np.array(d_rois.shape)